Locus 4271

Sequence ID 3R_DroMel_CAF1
Location 11,399,817 – 11,400,094
Length 277
Max. P 0.987468
window6933 window6934 window6935 window6936

overview

Window 3

Location 11,399,817 – 11,399,935
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 84.79
Mean single sequence MFE -40.04
Consensus MFE -25.10
Energy contribution -27.62
Covariance contribution 2.52
Combinations/Pair 1.14
Mean z-score -2.80
Structure conservation index 0.63
SVM decision value 1.05
SVM RNA-class probability 0.906938
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11399817 118 - 27905053
CAAGUGCGGCAACCUGCUGAGCUUGGCCAAUUGGGUCAGCUUAGG-GGAGUUUGGAAAAUAAAGAGGGUGUUGGAUUAGCGGCUUGGUGGUGUAAACUGCAGCUGC-AGUUGACAAGAAA
(((.((((((..(((.(((((((.((((.....))))))))))))-))((((((.(..((....(((.(((((...))))).))).))..).))))))...)))))-).)))........ ( -40.70)
>DroSec_CAF1 147493 119 - 1
CAAGUGCGGCAACCUGCUGAGCUUGGCCAAUUGGGUCAGCUUAGGGGGAGUUUGGAAAAUAAAGAGGGUGUUAGAUUAGGGGCUUGAUGCUGUAAGCUGCAGCUGC-AGUUGACAAUAAA
(((.((((((..(((.(((((((.((((.....))))))))))).)))..............................(.((((((......)))))).).)))))-).)))........ ( -42.90)
>DroSim_CAF1 138575 119 - 1
CAAGUGCGGCAACCUACUGAGCUUGGCCAAUUGGGUCAGCUUAGGGGGAGCUUGGAAAAUAAAGAGGGUGUUAGAUUAGCGGCUUGGUGGUGUAAGCUGCAGCUGC-AGUUGACAAUAAA
(((.((((((..((..(((((((.((((.....)))))))))))..))((((((.(..((....(((.(((((...))))).))).))..).))))))...)))))-).)))........ ( -45.20)
>DroEre_CAF1 135599 117 - 1
AAAGUGCUGCAACCUGCUGAGCUUGGCCAAUUGGGUCAGCUUGGG--GCUUUUGGUAAAUAAAGAGGGUGUUAGAUUAGCGGCUUGGUUGUGUAAGCGGCAGCUGCAAGUUGACAGCA-A
....(((((((((..((((.(((((..((((..((((.((((((.--((((((..(....)..)))))).)))....)))))))..))))..)))))..)))).....)))).)))))-. ( -42.00)
>DroYak_CAF1 138545 105 - 1
CAAGUGCCGCAACCUGCUGAGCUUGGCCAAUUGGGUCAGCUUGGG-GGCUUUGGGAAAACAGGAAGGGUGUUGGAUUAGCGGCUUAGUUGUGUA-------------AGUUGACAGGG-A
.....(((((..(((.(..((((.((((.....))))))))..))-))((((.(.....)..))))............)))))....((.(((.-------------.....))).))-. ( -29.40)
>consensus
CAAGUGCGGCAACCUGCUGAGCUUGGCCAAUUGGGUCAGCUUAGG_GGAGUUUGGAAAAUAAAGAGGGUGUUAGAUUAGCGGCUUGGUGGUGUAAGCUGCAGCUGC_AGUUGACAAGAAA
(((.((((((.((((.(((((((.((((.....)))))))))))......(((........))).)))).........((((((((......)))))))).))))).).)))........ (-25.10 = -27.62 +   2.52)

alignment

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secondary structure

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dotplot

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Window 4

Location 11,399,895 – 11,400,014
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.90
Mean single sequence MFE -37.71
Consensus MFE -32.44
Energy contribution -32.36
Covariance contribution -0.08
Combinations/Pair 1.10
Mean z-score -1.65
Structure conservation index 0.86
SVM decision value 1.26
SVM RNA-class probability 0.937850
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11399895 119 - 27905053
CCAGCAGAAGAAUCAGCCGGAAGCUGAAAGAACU-UUGCAGUGGAAAAAUAUAGUACACGAGUAUCUUGUGGAUGCGACGCAAGUGCGGCAACCUGCUGAGCUUGGCCAAUUGGGUCAGC
.((((((.....((((.(....))))).......-((((.(((.............)))..(((.((((((.......))))))))).)))).)))))).(((.((((.....))))))) ( -38.32)
>DroSec_CAF1 147572 120 - 1
CCAGCAGAAGAAUCAGCCGGAAGCUGAAAGAACUUUUGCAGUGGAAAAAUAUAAUACACGAGUAUCUUGUGGAUGCGACGCAAGUGCGGCAACCUGCUGAGCUUGGCCAAUUGGGUCAGC
.((((((.....((((.(....)))))........((((.(((.............)))..(((.((((((.......))))))))).)))).)))))).(((.((((.....))))))) ( -38.32)
>DroSim_CAF1 138654 120 - 1
CCAGCAGAAGAAUCAGCCGGAAGCUGAAAGAACUUUUGCAGUGGAAAAAUAUAGUACACGAGUAUCUUUUGGAUGCGACGCAAGUGCGGCAACCUACUGAGCUUGGCCAAUUGGGUCAGC
...(((((((..((((.(....))))).....)))))))(((((.........((((.((.(((((.....)))))..))...))))(....))))))..(((.((((.....))))))) ( -35.20)
>DroEre_CAF1 135676 119 - 1
CCAGCAGAAGAAUCAGCCGGAAGCUGAAAGAAAU-GCGCAGUGGAAGAAUAUAGAACACGAGUAUCUUGUGGAUGCGGGGAAAGUGCUGCAACCUGCUGAGCUUGGCCAAUUGGGUCAGC
.((((((.....((((.(....)))))......(-((((((((.............)))..(((((.....)))))........))).)))..)))))).(((.((((.....))))))) ( -36.52)
>DroYak_CAF1 138610 119 - 1
CCAGCAGAAGAAUCAGCCGGCAGCUGAAAGAAAC-UCGCAGUGGAGAAAUAUAGUAUUCGAGUAUCUUGUGGAUGCGGGGCAAGUGCCGCAACCUGCUGAGCUUGGCCAAUUGGGUCAGC
.((((((.....(((((.....)))))((((.((-(((.((((.(....)....))))))))).)))).....(((((.(....).)))))..)))))).(((.((((.....))))))) ( -40.20)
>consensus
CCAGCAGAAGAAUCAGCCGGAAGCUGAAAGAACU_UUGCAGUGGAAAAAUAUAGUACACGAGUAUCUUGUGGAUGCGACGCAAGUGCGGCAACCUGCUGAGCUUGGCCAAUUGGGUCAGC
.((((((.....(((((.....)))))..........((.(((.............)))..(((((.....)))))..(((....)))))...)))))).(((.((((.....))))))) (-32.44 = -32.36 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,399,975 – 11,400,094
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.65
Mean single sequence MFE -19.57
Consensus MFE -15.21
Energy contribution -14.97
Covariance contribution -0.24
Combinations/Pair 1.04
Mean z-score -1.82
Structure conservation index 0.78
SVM decision value 0.44
SVM RNA-class probability 0.737245
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11399975 119 + 27905053
UGCAA-AGUUCUUUCAGCUUCCGGCUGAUUCUUCUGCUGGCUGCUUCAAAAAUUACAUUAAACAUACUUUUAUUUAAUUCUCGCUUUCCAGCCACCCCCUUGACCAACAUCCCACUUCGG
.((((-((.....(((((.....)))))..))).)))((((((.......(((((...((((......))))..))))).........)))))).......................... ( -17.49)
>DroSec_CAF1 147652 120 + 1
UGCAAAAGUUCUUUCAGCUUCCGGCUGAUUCUUCUGCUGGCUGCUUCAAAAAUUACAUUAAACAUACUUUUAUUUAAUUCUCGCUUUCCAGCCACCCCCUUGACCAUCAUCCCACUUCUG
.(((.(((.....(((((.....)))))..))).)))((((((.......(((((...((((......))))..))))).........)))))).......................... ( -18.69)
>DroSim_CAF1 138734 120 + 1
UGCAAAAGUUCUUUCAGCUUCCGGCUGAUUCUUCUGCUGGCUGCUUCAAAAAUUACAUUAAACAUACUUUUAUUUAAUUCUCGCUUUCCAGCCACCCCCUUGACCAUCAUCCCACUUCUG
.(((.(((.....(((((.....)))))..))).)))((((((.......(((((...((((......))))..))))).........)))))).......................... ( -18.69)
>DroEre_CAF1 135756 119 + 1
UGCGC-AUUUCUUUCAGCUUCCGGCUGAUUCUUCUGCUGGCUGCUUCAAAAAUUACAUUAAACAUACUUUUAUUUAAUUCUCGCUCCCCAGCCACCCUCUUGACCAUCAUCCCACUUCGG
...((-(......(((((.....)))))......)))((((((.......(((((...((((......))))..))))).........)))))).......................... ( -17.29)
>DroYak_CAF1 138690 116 + 1
UGCGA-GUUUCUUUCAGCUGCCGGCUGAUUCUUCUGCUGGCUGCUUCAGAAAUUACAUUAAACAUACUUUUAUUUAAUUCUCGCUUUGCAGCCACCCUCUUGACCAUCAACCCACU---G
.((((-((((((...(((.((((((.((....)).)))))).)))..)))))....((((((.(......).)))))).)))))................................---. ( -25.70)
>consensus
UGCAA_AGUUCUUUCAGCUUCCGGCUGAUUCUUCUGCUGGCUGCUUCAAAAAUUACAUUAAACAUACUUUUAUUUAAUUCUCGCUUUCCAGCCACCCCCUUGACCAUCAUCCCACUUCGG
.(((.........(((((.....)))))......)))((((((.......(((((...((((......))))..))))).........)))))).......................... (-15.21 = -14.97 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,399,975 – 11,400,094
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.65
Mean single sequence MFE -29.96
Consensus MFE -24.42
Energy contribution -24.38
Covariance contribution -0.04
Combinations/Pair 1.04
Mean z-score -2.41
Structure conservation index 0.82
SVM decision value 2.08
SVM RNA-class probability 0.987468
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11399975 119 - 27905053
CCGAAGUGGGAUGUUGGUCAAGGGGGUGGCUGGAAAGCGAGAAUUAAAUAAAAGUAUGUUUAAUGUAAUUUUUGAAGCAGCCAGCAGAAGAAUCAGCCGGAAGCUGAAAGAACU-UUGCA
((......))......(.(((((.(.((((((.....(((((((((..((((......))))...)))))))))...)))))).).......((((.(....))))).....))-)))). ( -28.90)
>DroSec_CAF1 147652 120 - 1
CAGAAGUGGGAUGAUGGUCAAGGGGGUGGCUGGAAAGCGAGAAUUAAAUAAAAGUAUGUUUAAUGUAAUUUUUGAAGCAGCCAGCAGAAGAAUCAGCCGGAAGCUGAAAGAACUUUUGCA
(((((((.................(.((((((.....(((((((((..((((......))))...)))))))))...)))))).).......((((.(....)))))....))))))).. ( -29.60)
>DroSim_CAF1 138734 120 - 1
CAGAAGUGGGAUGAUGGUCAAGGGGGUGGCUGGAAAGCGAGAAUUAAAUAAAAGUAUGUUUAAUGUAAUUUUUGAAGCAGCCAGCAGAAGAAUCAGCCGGAAGCUGAAAGAACUUUUGCA
(((((((.................(.((((((.....(((((((((..((((......))))...)))))))))...)))))).).......((((.(....)))))....))))))).. ( -29.60)
>DroEre_CAF1 135756 119 - 1
CCGAAGUGGGAUGAUGGUCAAGAGGGUGGCUGGGGAGCGAGAAUUAAAUAAAAGUAUGUUUAAUGUAAUUUUUGAAGCAGCCAGCAGAAGAAUCAGCCGGAAGCUGAAAGAAAU-GCGCA
((....(((........)))...)).((((((.....(((((((((..((((......))))...)))))))))...))))))(((......((((.(....)))))......)-))... ( -27.40)
>DroYak_CAF1 138690 116 - 1
C---AGUGGGUUGAUGGUCAAGAGGGUGGCUGCAAAGCGAGAAUUAAAUAAAAGUAUGUUUAAUGUAAUUUCUGAAGCAGCCAGCAGAAGAAUCAGCCGGCAGCUGAAAGAAAC-UCGCA
.---.((.(((((((..((.....(.(((((((..((.((..((((((((......))))))))....)).))...))))))).).))...))))))).)).((.((.......-)))). ( -34.30)
>consensus
CAGAAGUGGGAUGAUGGUCAAGGGGGUGGCUGGAAAGCGAGAAUUAAAUAAAAGUAUGUUUAAUGUAAUUUUUGAAGCAGCCAGCAGAAGAAUCAGCCGGAAGCUGAAAGAACU_UUGCA
.....(((................(.((((((.....(((((((((..((((......))))...)))))))))...)))))).).......(((((.....))))).........))). (-24.42 = -24.38 +  -0.04)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:24:08 2006